DNA segments carrying linked genes from the genome of transformable B. subtilis are fractionated by agarose gel electrophoresis following cleavage by restriction endonucleases. The selected segments are then ligated to plasmid vectors and amplified in a recombination deficient strain of B. subtilis. The cloned gene sequence will then be used as donor DNA for transformation. Thus these molecules are homogenous with regard to size, sequence, ends and genetic constitution. Biochemical alteration of these molecules during entry into the cell and their physical incorporation into the resident genome are to be analyzed. Several recombination deficient mutants will be employed to pinpoint the blocked steps in recombination. In addition, the role of defective phage and cryptic genes' expression in B. subtilis will be elucidated. Recently we showed one such gene produces a DNA methylase during transformation stage of the cell.